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- EMDB-42983: Structure of the Human Respirovirus 3 Fusion Protein Bound to Cam... -

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Basic information

Entry
Database: EMDB / ID: EMD-42983
TitleStructure of the Human Respirovirus 3 Fusion Protein Bound to Camelid Nanobodies 4C03 and 4C06
Map dataFinal refinement volume. DeepEMhancer sharpened. Used for building coordinates.
Sample
  • Complex: Prefusion Human Respirovirus 3 Fusion Protein bound to Camelid nanobodies 4C03 and 4C06
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: Camelid Nanobody 4C03
    • Protein or peptide: Camelid Nanobody 4C06
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsviral fusion protein / camelid nanobodies / viral glycoprotein / membrane fusion / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / plasma membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesHuman respirovirus 3 / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsJohnson NV / Ramamohan AR / McLellan JS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for potent neutralization of human respirovirus type 3 by protective single-domain camelid antibodies.
Authors: Nicole V Johnson / Revina C van Scherpenzeel / Mark J G Bakkers / Ajit R Ramamohan / Daan van Overveld / Lam Le / Johannes P M Langedijk / Joost A Kolkman / Jason S McLellan /
Abstract: Respirovirus 3 is a leading cause of severe acute respiratory infections in vulnerable human populations. Entry into host cells is facilitated by the attachment glycoprotein and the fusion ...Respirovirus 3 is a leading cause of severe acute respiratory infections in vulnerable human populations. Entry into host cells is facilitated by the attachment glycoprotein and the fusion glycoprotein (F). Because of its crucial role, F represents an attractive therapeutic target. Here, we identify 13 F-directed heavy-chain-only antibody fragments that neutralize recombinant respirovirus 3. High-resolution cryo-EM structures of antibody fragments bound to the prefusion conformation of F reveal three distinct, previously uncharacterized epitopes. All three antibody fragments bind quaternary epitopes on F, suggesting mechanisms for neutralization that may include stabilization of the prefusion conformation. Studies in cotton rats demonstrate the prophylactic efficacy of these antibody fragments in reducing viral load in the lungs and nasal passages. These data highlight the potential of heavy-chain-only antibody fragments as effective interventions against respirovirus 3 infection and identify neutralizing epitopes that can be targeted for therapeutic development.
History
DepositionNov 30, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42983.png

Downloads & links

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Map

FileDownload / File: emd_42983.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal refinement volume. DeepEMhancer sharpened. Used for building coordinates.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 320 pix.
= 300.8 Å		0.94 Å/pix.
x 320 pix.
= 300.8 Å		0.94 Å/pix.
x 320 pix.
= 300.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.035332188 - 1.5254257
Average (Standard dev.)0.0010358801 (±0.021555087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 300.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Final refined volume. Sharpened map. Not DeepEMhancer sharpened.

Fileemd_42983_additional_1.map
AnnotationFinal refined volume. Sharpened map. Not DeepEMhancer sharpened.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_42983_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_42983_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Prefusion Human Respirovirus 3 Fusion Protein bound to Camelid na...

EntireName: Prefusion Human Respirovirus 3 Fusion Protein bound to Camelid nanobodies 4C03 and 4C06
Components
  • Complex: Prefusion Human Respirovirus 3 Fusion Protein bound to Camelid nanobodies 4C03 and 4C06
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: Camelid Nanobody 4C03
    • Protein or peptide: Camelid Nanobody 4C06
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Prefusion Human Respirovirus 3 Fusion Protein bound to Camelid na...

SupramoleculeName: Prefusion Human Respirovirus 3 Fusion Protein bound to Camelid nanobodies 4C03 and 4C06
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Human respirovirus 3
Molecular weightTheoretical: 277 KDa

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Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human respirovirus 3
Molecular weightTheoretical: 55.364965 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QIDITKLQHV GVLVNSPKGM KISQNFETRY LILSLIPKIE DSNSCGDQQI KQYKRLLDRL IIPLYDGLRL QKDVIVTNQE SNENTDPRT ERFFGGVIGT IALGVATSAQ ITAAVALVEA KQARSDIEKL KEAIRDTNKA VQSVQSSPGN LIVAIKSVQD Y VNKEIVPC ...String:
QIDITKLQHV GVLVNSPKGM KISQNFETRY LILSLIPKIE DSNSCGDQQI KQYKRLLDRL IIPLYDGLRL QKDVIVTNQE SNENTDPRT ERFFGGVIGT IALGVATSAQ ITAAVALVEA KQARSDIEKL KEAIRDTNKA VQSVQSSPGN LIVAIKSVQD Y VNKEIVPC IARLGCEACG LLLGLALDQH YSELTNIFGD NIGSLQEKGI KLQGIASLYR TNITEIFTTS TVDKYDIYDL LF TESIKVR VIDVDLNDYS ITLQVRLPLL TRLLNTQIYK VDSISYNIQN REWYIPLPSH IMTKGAFLGG ADVKECIEAF SSY ICPSDP GFVLNHEMES CLSGNISQCP RTTVTSDIVP RYAFVNGGVV ANCITTTCTC NGIGNRINQP PDQGVKIITH KECN TIGIN GMLFNTNKEG TLAFYTPDDI TLNNSVALNP IDISIELNKA KSDLEESKEW IRRSNQKLDS IEDKIEEILS KIYHI ENEI ARIKKLIGEA EPEA

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: Camelid Nanobody 4C03

MacromoleculeName: Camelid Nanobody 4C03 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.726373 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EVQLVESGGG LVRAGGSLRL SCAASLRDLH TRTFYMGWFR QDPGKEREFV AAIDWNTGAA SYPDSVKGRF TISKDNARNA VYLQMNNLK PEDTAVYYCA VGRPPLNRPT LAYYWGQGTQ VTVSS

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Macromolecule #3: Camelid Nanobody 4C06

MacromoleculeName: Camelid Nanobody 4C06 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 12.487816 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EVQLVESGGG LVQPGGSLRL SCSASGSLST IKALGWYRRA PGRERELVAS ITSAGETNYA DSAKGRFTVS TDNAKNTVDL RMNSLKPED TAVYYCYAES FVLNIYWGQG TQVTVSSG

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 336418
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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